The a-SiOx thin films with silicon nanoclusters are currently being actively studied by various laboratories due to the possibility of efficient control of their optical properties, both at the stage of formation and using technological treatments. The presence of excess silicon in such films leads to the growth of nanocrystals during high-temperature annealing, which affects the optical properties of SiOx films, including photoluminescence. Therefore, in this work, we studied the formation of silicon nanocrystals in a-SiOx films during Pulse Photon Annealing (PPA). X-ray diffraction studies of SiOx films with different silicon contents have shown that, upon PPA annealing, arrays of silicon nanocrystals of significantly different average sizes are formed. Moreover, according to the Raman spectroscopy data, PPA does not lead to complete ordering of the structural network of silicon atoms, and some of the atoms, apparently located in small clusters of ~1 nm, retain deviations from interatomic distances and bond angles.